BN1756 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.3606e-07 2.4549e-05
Layer 3 1.9924e-06 3.0185e-04
Layer 5 9.3487e-06 1.0482e-04
Layer 6 6.0779e-05 4.0262e-03
Layer 2 3.6845e-04 4.8889e-02
Layer 1 6.1874e-01 6.1785e-01
WM 7.1226e-01 5.4923e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
CHGA Expression Distribution
Gene Specificity Score (GSS)
CHGA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
CHGA Layer 4 2.8516 0.8309
GABRG2 Layer 4 3.0781 0.8291
CPLX1 Layer 5 3.1387 0.8282
MAPK10 Layer 4 2.7715 0.8228
SOD2 Layer 4 2.7363 0.8226
DCLK1 Layer 4 2.8799 0.8223
TOLLIP Layer 5 2.8652 0.8222
CEND1 Layer 4 2.8594 0.8218
INPP5F Layer 4 3.0996 0.8187
TUBB3 Layer 5 2.8281 0.8181
BEX5 Layer 4 2.9375 0.8180
BMERB1 Layer 5 2.8516 0.8177
NSG1 Layer 4 2.9023 0.8172
PFKP Layer 4 3.0918 0.8167
NCALD Layer 5 3.0059 0.8166
CAMK2G Layer 4 2.8086 0.8159
TRIM37 Layer 5 2.9727 0.8148
NUAK1 Layer 4 3.2461 0.8147
LINGO1 Layer 4 2.9502 0.8138
ARL8B Layer 4 2.7275 0.8136
SNX10 Layer 5 2.8027 0.8135
INA Layer 4 3.0283 0.8131
SULT4A1 Layer 4 2.9668 0.8124
ELAVL4 Layer 5 2.9668 0.8119
STX1B Layer 4 3.0996 0.8118
HK1 Layer 4 2.7451 0.8115
MAP1LC3A Layer 5 2.5449 0.8109
DDX24 Layer 4 2.7246 0.8108
SYNGR1 Layer 5 2.9277 0.8104
PIN1 Layer 5 2.5957 0.8100
NAP1L2 Layer 4 3.0000 0.8099
SPINT2 Layer 4 2.8906 0.8095
SIRPA Layer 5 2.5508 0.8093
ATP6V1G2 Layer 5 2.8340 0.8091
SATB1 Layer 4 3.1797 0.8087
MAPT Layer 5 2.6836 0.8086
CADM3 Layer 4 2.8496 0.8082
ATP13A2 Layer 5 2.9473 0.8080
ATP6V1B2 Layer 5 2.7852 0.8078
RAB3A Layer 5 2.6367 0.8078
SV2A Layer 5 2.8281 0.8074
SCN1B Layer 4 3.7402 0.8070
DYNC1H1 Layer 5 2.5176 0.8068
FXYD7 Layer 4 3.0000 0.8067
SYT4 Layer 5 2.7793 0.8066
CAPNS1 Layer 5 2.6191 0.8058
ANXA6 Layer 5 3.0781 0.8058
NDRG4 Layer 4 2.6191 0.8056
MYO5A Layer 4 2.9219 0.8051
NAPA Layer 4 2.6895 0.8047

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1756
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1756_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1756/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1756/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1756/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1756/report/PD/BN1756_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1756/report/PD/BN1756_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:06:02
  • Number of Processes: 10
  • Spending Time: 0h 4m